Hi, Zhijin,
Thanks for your explanation and I am going to take expression value from
most recent version.
JongMin



On 2/5/08, Zhijin Wu <zwu@stat.brown.edu> wrote:
>
> We did make differences on the gcRMA when we updated from 1.x.x to the
> 2.x.x versions. Different results are expected because of the change in
> background estimation. However, assessment on the calibration data (two
> latin square datasets) showed that there is not much practical
> differences. For two samples, the differences in expression values from
> two different versions of gcrma should still be close to identical. (For
> example, you may see one gene used to be 6 and 6.1 across two samples
> and became 5 and 5.1 in another version, but the differences in
> expression are both .1).
>
> JONG-MIN LEE wrote:
> > Hi, all,
> > I just found gcRMA expression values for U133p2 arrays are different
> > depending on platform and version.
> > I compared two gcRMA expression values and they were quite different.
> > The first one was by is R2.6.0, gcRMA 2.10.0, on Unix.
> > The second one was obtained by R2.4.0, gcRMA 1.6.0, on WIndows XP.
> > So, there was nothing in common between two, and I didn't try to figure
> out
> > whether the difference came form platform difference or version
> difference
> > (R or gcrma).
> > Nonetheless, I was expecting consistent results regardless of platform
> of
> > version.
> > Has anyone noticed this?
> > Thanks.
> > JongMIn
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> -------------------------------------------
> Zhijin (Jean) Wu
> Assistant Professor of Biostatistics
> Brown University, Box G-S121
> Providence, RI  02912
>
> Tel: 401 863 1230
> Fax: 401 863 9182
> http://stat.brown.edu/~zwu
>
>

	[[alternative HTML version deleted]]

